The homogeneous charge compression ignition, HCCI, uses compression ignition to auto-ignite a homogeneous air/fuel mixture. Using internally trapped engine exhaust gas, IEGR, as an indirect control method, HCCI offers superior fuel economy and pollutant emission reductions. Fuel structure has direct impact on its auto-ignition performance. In this research, the effect of IEGR on auto-ignition timing of four typical fuels with distinct Octane number: N-heptane, Iso-octane, Ethanol and Methane have been studied using a single zone adiabatic combustion model and detailed chemical kinetics. It was found that the introduction of internal exhaust gas recirculation, IEGR, delays ignition timing of all four fuels, but differently. N-heptane is the most sensitive fuel to IEGR, iso-octane and ethanol has a much higher endurance, while methane is somewhere in between.